In much the way I am aware of the Windows store: I avoid it and work to get the software directly from the source.
That is not the way things work on Linux - the repos essentially are the source. It is intended for apps to be packaged and distributed through official repos precisely to avoid the issues you listed, which are more often issues of downloading from sites. Package managers take care of incompatible versions and conflicts. That's definitely a Windows bias my friend :P
Mutual aid, free association, common ownership of the means of production, coalescing into a society where people contribute out of genuine gratitude to be part of it